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Frequency-control of protein translocation across an oscillating nanopore

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Abstract

The translocation of a lipid binding protein (LBP) is studied using a phenomenological coarse-grained computational model that simplifies both chain and pore geometry. We investigated via molecular dynamics the interplay between transport and unfolding in the presence of a nanopore whose section oscillates periodically in time with a frequency ω, a motion often referred to as the radial breathing mode (RBM). We found that the LPB when mechanically pulled into the vibrating nanopore exhibits a translocation dynamics that in some frequency range is accelerated and shows a frequency locking to the pore dynamics. The main effect of pore vibrations is the suppression of stalling events of the translocation dynamics, hence, proper frequency tuning allows both regularization and control of the overall transport process. Finally, the interpretation of the simulation results is easily achieved by resorting to a first passage theory of elementary driven-diffusion processes.

Graphical abstract: Frequency-control of protein translocation across an oscillating nanopore

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Publication details

The article was received on 29 Nov 2016, accepted on 30 Mar 2017 and first published on 31 Mar 2017


Article type: Paper
DOI: 10.1039/C6CP08156H
Citation: Phys. Chem. Chem. Phys., 2017, Advance Article
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    Frequency-control of protein translocation across an oscillating nanopore

    F. Cecconi, M. A. Shahzad, U. Marini Bettolo Marconi and A. Vulpiani, Phys. Chem. Chem. Phys., 2017, Advance Article , DOI: 10.1039/C6CP08156H

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